/// <summary>
/// Validate input graph.
/// Throws exception if graph is null.
/// </summary>
/// <param name="graph">Input graph.</param>
public static void ValidateGraph(ContigGraph graph)
{
if (graph == null)
{
throw new ArgumentNullException("graph");
}
}
/// <summary>
/// Validate input graph.
/// Throws exception if graph is null.
/// </summary>
/// <param name="graph">Input graph.</param>
public static void ValidateGraph(ContigGraph graph)
{
if (graph == null)
{
throw new ArgumentNullException("graph");
}
}
/// <summary>
/// Performs Breadth First Search to traverse through graph to generate scaffold paths.
/// </summary>
/// <param name="overlapGraph">Contig Overlap Graph.</param>
/// <param name="contigPairedReadMaps">InterContig Distances.</param>
/// <param name="lengthOfKmer">Length of Kmer.</param>
/// <param name="searchDepth">Depth to which graph is searched.</param>
/// <returns>List of paths/scaffold.</returns>
public IList<ScaffoldPath> FindPaths(
ContigGraph overlapGraph,
ContigMatePairs contigPairedReadMaps,
int lengthOfKmer,
int searchDepth = 10)
{
if (overlapGraph == null)
{
throw new ArgumentNullException("deBruijnGraph");
}
if (contigPairedReadMaps == null)
{
throw new ArgumentNullException("contigPairedReadMaps");
}
if (lengthOfKmer <= 0)
{
throw new ArgumentException(Resource.KmerLength);
}
if (searchDepth <= 0)
{
throw new ArgumentException(Resource.Depth);
}
this.graph = overlapGraph;
this.kmerLength = lengthOfKmer;
this.depth = searchDepth;
List<ScaffoldPath> scaffoldPaths = new List<ScaffoldPath>();
Parallel.ForEach(
overlapGraph.Nodes,
(Node node) =>
{
Dictionary<ISequence, IList<ValidMatePair>> contigPairedReadMap;
if (contigPairedReadMaps.TryGetValue(overlapGraph.GetNodeSequence(node), out contigPairedReadMap))
{
List<ScaffoldPath> scaffoldPath = TraverseGraph(node, contigPairedReadMap);
lock (scaffoldPaths)
{
scaffoldPaths.AddRange(scaffoldPath);
}
}
});
return scaffoldPaths;
}
/// <summary>
/// Generate sequences from list of contig nodes.
/// </summary>
/// <param name="contigGraph">Contig Overlap Graph.</param>
/// <param name="paths">Scaffold paths.</param>
/// <returns>List of sequences of scaffolds.</returns>
protected IList<ISequence> GenerateScaffold(
ContigGraph contigGraph,
IList<ScaffoldPath> paths)
{
if (contigGraph == null)
{
throw new ArgumentNullException("contigGraph");
}
if (paths == null)
{
throw new ArgumentNullException("paths");
}
List<ISequence> scaffolds = paths.AsParallel().Select(t => t.BuildSequenceFromPath(contigGraph, this.kmerLength)).ToList();
IEnumerable<Node> visitedNodes = contigGraph.Nodes.AsParallel().Where(t => !t.IsMarked());
scaffolds.AddRange(visitedNodes.AsParallel().Select(t => contigGraph.GetNodeSequence(t)));
contigGraph.Dispose();
return scaffolds;
}
/// <summary>
/// Performs Breadth First Search in contig overlap graph.
/// </summary>
/// <param name="contigGraph">Contig Graph.</param>
/// <param name="contigMatePairs">Contig Mate Pair map.</param>
/// <returns>List of Scaffold Paths.</returns>
protected IList<ScaffoldPath> TracePath(ContigGraph contigGraph, ContigMatePairs contigMatePairs)
{
return this.tracePath.FindPaths(contigGraph, contigMatePairs, this.kmerLength, this.depthField);
}
/// <summary>
/// Generate contig overlap graph.
/// </summary>
/// <param name="contigs">List of contig sequences.</param>
/// <returns>Contig Graph.</returns>
protected ContigGraph GenerateContigOverlapGraph(IList<ISequence> contigs)
{
if (contigs == null)
{
throw new ArgumentNullException("contigs");
}
ContigGraph contigGraph = new ContigGraph();
contigGraph.BuildContigGraph(contigs, this.kmerLength);
return contigGraph;
}
public void TracePathTestWithPalindromicContig()
{
const int kmerLengthConst = 5;
const int dangleThreshold = 3;
const int redundantThreshold = 6;
var sequences = new List<ISequence>()
{
new Sequence(Alphabets.DNA, "ATGCCTC") {ID = "0"},
new Sequence(Alphabets.DNA, "CCTCCTAT") {ID = "1"},
new Sequence(Alphabets.DNA, "TCCTATC") {ID = "2"},
new Sequence(Alphabets.DNA, "TGCCTCCT") {ID = "3"},
new Sequence(Alphabets.DNA, "ATCTTAGC") {ID = "4"},
new Sequence(Alphabets.DNA, "CTATCTTAG") {ID = "5"},
new Sequence(Alphabets.DNA, "CTTAGCG") {ID = "6"},
new Sequence(Alphabets.DNA, "GCCTCCTAT") {ID = "7"},
new Sequence(Alphabets.DNA, "TAGCGCGCTA") {ID = "8"},
new Sequence(Alphabets.DNA, "AGCGCGC") {ID = "9"},
new Sequence(Alphabets.DNA, "TTTTTT") {ID = "10"},
new Sequence(Alphabets.DNA, "TTTTTAAA") {ID = "11"},
new Sequence(Alphabets.DNA, "TAAAAA") {ID = "12"},
new Sequence(Alphabets.DNA, "TTTTAG") {ID = "13"},
new Sequence(Alphabets.DNA, "TTTAGC") {ID = "14"},
new Sequence(Alphabets.DNA, "GCGCGCCGCGCG") {ID = "15"},
};
KmerLength = kmerLengthConst;
SequenceReads.Clear();
SetSequenceReads(sequences);
CreateGraph();
DanglingLinksThreshold = dangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(dangleThreshold);
RedundantPathLengthThreshold = redundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(redundantThreshold);
UnDangleGraph();
RemoveRedundancy();
IList<ISequence> contigs = BuildContigs().ToList();
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(contigs, sequences, kmerLengthConst);
MatePairMapper builder = new MatePairMapper();
CloneLibrary.Instance.AddLibrary("abc", 5, 15);
ContigMatePairs pairedReads = builder.MapContigToMatePairs(sequences, maps);
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs overlap = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(overlap);
overlap = dist.CalculateDistance();
ContigGraph graph = new ContigGraph();
graph.BuildContigGraph(contigs, this.KmerLength);
TracePath path = new TracePath();
IList<ScaffoldPath> paths = path.FindPaths(graph, overlap, kmerLengthConst, 3);
Assert.AreEqual(paths.Count, 3);
Assert.AreEqual(paths.First().Count, 3);
ScaffoldPath scaffold = paths.First();
Assert.AreEqual("ATGCCTCCTATCTTAGC", graph.GetNodeSequence(scaffold[0].Key).ConvertToString());
Assert.AreEqual("TTAGCGCG", graph.GetNodeSequence(scaffold[1].Key).ConvertToString());
Assert.AreEqual("GCGCGC", graph.GetNodeSequence(scaffold[2].Key).ConvertToString());
}
/// <summary>
/// Validate scaffold paths for a given input reads.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateScaffoldPath(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.RedundantThreshold);
string[] expectedScaffoldNodes = utilityObj.xmlUtil.GetTextValues(nodeName,Constants.ScaffoldNodes);
string libraray = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.LibraryName);
string stdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.Mean);
string expectedDepth = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.DepthNode);
// Get the input reads and build kmers
using (FastAParser parser = new FastAParser(filePath))
{
IEnumerable<ISequence> sequenceReads = parser.Parse();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, null);
this.DanglingLinksPurger = new DanglingLinksPurger(Int32.Parse(daglingThreshold, null));
this.RedundantPathsPurger = new RedundantPathsPurger(Int32.Parse(redundantThreshold, null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
ContigGraph graph = new ContigGraph();
this.UnDangleGraph();
// Build contig.
this.ContigBuilder = new SimplePathContigBuilder();
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
IList<ISequence> sortedContigs = SortContigsData(contigs.ToList());
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(sortedContigs, sequenceReads, this.KmerLength);
// Find map paired reads.
CloneLibrary.Instance.AddLibrary(libraray, float.Parse(mean, null), float.Parse(stdDeviation, null));
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequenceReads, maps);
// Filter contigs based on the orientation.
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(contigpairedReads);
dist.CalculateDistance();
graph.BuildContigGraph(contigs.ToList(), this.KmerLength);
// Validate ScaffoldPath using BFS.
TracePath trace = new TracePath();
IList<ScaffoldPath> paths = trace.FindPaths(graph, contigpairedReads, Int32.Parse(kmerLength, null),
Int32.Parse(expectedDepth, null));
ScaffoldPath scaffold = paths.First();
foreach (KeyValuePair<Node, Edge> kvp in scaffold)
{
ISequence seq = graph.GetNodeSequence(kvp.Key);
string sequence = seq.ConvertToString();
string reversedSequence = seq.GetReverseComplementedSequence().ConvertToString();
Assert.IsTrue(expectedScaffoldNodes.Contains(sequence)
|| expectedScaffoldNodes.Contains(reversedSequence),
"Failed to find " + sequence + ", or " + reversedSequence);
}
}
ApplicationLog.WriteLine("PADENA P1 : FindPaths() validation for Padena step6:step6 completed successfully");
}
/// <summary>
/// Validate Assembled paths for a given input reads.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateAssembledPath(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.RedundantThreshold);
string library = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.LibraryName);
string StdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Mean);
string expectedDepth = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DepthNode);
string[] assembledPath = utilityObj.xmlUtil.GetTextValues(nodeName, Constants.SequencePathNode);
// Get the input reads and build kmers
FastAParser parser = new FastAParser();
parser.Open(filePath);
IEnumerable<ISequence> sequenceReads = parser.Parse().ToList();
parser.Close ();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, null);
this.DanglingLinksPurger = new DanglingLinksPurger(Int32.Parse(daglingThreshold, null));
this.RedundantPathsPurger = new RedundantPathsPurger(Int32.Parse(redundantThreshold, null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
ContigGraph graph = new ContigGraph();
this.UnDangleGraph();
// Build contig.
this.ContigBuilder = new SimplePathContigBuilder();
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
IList<ISequence> sortedContigs = SortContigsData(contigs.ToList());
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(sortedContigs, sequenceReads, this.KmerLength);
// Find map paired reads.
CloneLibrary.Instance.AddLibrary(library, float.Parse(mean, null), float.Parse(StdDeviation, null));
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequenceReads, maps);
// Filter contigs based on the orientation.
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(contigpairedReads);
dist.CalculateDistance();
graph.BuildContigGraph(contigs.ToList(), this.KmerLength);
// Validate ScaffoldPath using BFS.
TracePath trace = new TracePath();
IList<ScaffoldPath> paths = trace.FindPaths(graph, contigpairedReads, Int32.Parse(kmerLength, null),
Int32.Parse(expectedDepth, null));
// Assemble paths.
PathPurger pathsAssembler = new PathPurger();
pathsAssembler.PurgePath(paths);
// Get sequences from assembled path.
IList<ISequence> seqList = paths.Select(temp => temp.BuildSequenceFromPath(graph, Int32.Parse(kmerLength, null))).ToList();
//Validate assembled sequence paths.
foreach (string sequence in seqList.Select(t => t.ConvertToString()))
{
Assert.IsTrue(assembledPath.Contains(sequence), "Failed to locate " + sequence);
}
ApplicationLog.WriteLine("PADENA P1 : AssemblePath() validation for Padena step6:step7 completed successfully");
}
public void ValidateBuildSequenceFromPath()
{
const int KmerLength = 7;
ISequence sequence = new Sequence(Alphabets.DNA, "GATTCAAGGGCTGGGGG");
ISequence sequenceNew;
IList<ISequence> contigsSequence = SequenceToKmerBuilder.GetKmerSequences(sequence, KmerLength).ToList();
using (ContigGraph graph = new ContigGraph())
{
graph.BuildContigGraph(contigsSequence, KmerLength);
List<Node> contigs = graph.Nodes.ToList();
ScaffoldPath path = new ScaffoldPath();
foreach (Node node in contigs.GetRange(0, 11))
{
path.Add(new KeyValuePair<Node, Edge>(node, new Edge(true)));
}
sequenceNew = path.BuildSequenceFromPath(graph, KmerLength);
}
Assert.IsNotNull(sequenceNew);
Assert.AreEqual((new string(sequenceNew.Select(a => (char)a).ToArray())), "GATTCAAGGGCTGGGGG");
}
